Changing input of DNA sequence types to DNAStringSet
Edited DNA reference object to make use of Biostrings sequences instead of DNAbin

TODO: Make sure that subsequent HybRIDS stages take into account this
fundamental change in how sequences are stored and dealt with.
Rewritten SSscan to take advantage of the types and methods provided by Biostrings
Documentation and some code update
Completed required alterations for dating function required for new sequence types
Added man folder to gitignore as manpages are built on users machine when package is installed
added .Rd files to gitignore
edited gitignore
Merge branch 'Larger-sequences'

Conflicts:
	R/DNAReference.R
Resolved conflicts